Proteome analysis of human CD56^neg NK cells reveals a homogeneous phenotype surprisingly similar to CD56^dim NK cells

Abstract

NK cells lacking CD56 (CD56 ) were first identified in chronic HIV-1 infection. However, CD56 NK cells also exist in healthy individuals, albeit in significantly lower numbers. Here, we provide an extensive proteomic characterisation of human CD56 peripheral blood NK cells of healthy donors and compare them to their CD56 and CD56 counterparts. Unbiased large-scale surface receptor profiling clustered CD56 cells as part of the main NK cell compartment and indicated an overall CD56 -like phenotype. Total proteome analyses of CD56 NK cells further confirmed their similarity with CD56 NK cells, and revealed a complete cytolytic inventory with high levels of perforin and granzyme H and M. In the present study, twelve proteins discriminated CD56 NK cells from CD56 NK cells with nine up-regulated and three down-regulated proteins in the CD56 NK cell population. Those proteins were functionally related to lytic granule composition and transport, interaction with the extracellular matrix, DNA transcription or repair, and proliferation. Corroborating these results, CD56 NK cells showed modest cytotoxicity, degranulation, and IFN-ɣ secretion as compared to CD56 NK cells. In conclusion, CD56 NK cells constitute functionally competent cells sharing many features of bona fide CD56 NK cells in healthy individuals, but with some distinct characteristics.

A New Hope for CD56negCD16pos NK Cells as Unconventional Cytotoxic Mediators: An Adaptation to Chronic Diseases

“…In fact, CD56 neg CD16 pos cells expressed multiple NK cell markers including KIRs, NKG2C, NKp30, CD16a, NKG2D, 2B4, CD57, TRAIL, CRTAM and CRACC. Moreover, our previous study highlighted the phenotypic similarities between these two NK cell subsets (Forconi et al, 2018) which was supported by the Voigt et.al proteomic study (Voigt et al, 2018). Together, these findings confirm that CD56 neg CD16 pos cells are true NK cells.…”

“…Most of the genes differentially expressed when comparing CD56 neg CD16 pos to CD56 dim CD16 pos NK cells that are highlighted in the RNA-sequencing experiment have already been described at the protein expression level in previous studies (Forconi et al, 2018;Voigt et al, 2018). CD56 dim CD16 pos compared to CD56 neg CD16 pos NK cells express less NKp80, IL18Ra, CD161, NKp46, DNAM1 with no differences for CD57, Perforin 1, CD11c, NKG2D, NKG2C and most of the KIRs.…”

“…More recently, we reported a dramatic expansion of CD56 neg CD16 pos NK cells in African children chronically/repeatedly infected with Plasmodium falciparum malaria and in those who were diagnosed with endemic Burkitt lymphoma (eBL) (Forconi et al, 2018). Proteomic analyses showed similarities between CD56 dim CD16 pos and CD56 neg CD16 pos NK cells (Voigt et al, 2018) thus supporting the classification of this subset as NK cells. Since CD56 neg CD16 pos NK cells are extremely low in American/European healthy adults (Supplemental Figure 1), most studies have focused on characterizing the function and therapeutic potential of CD56 bright and CD56 dim NK cell subsets.…”

Timing of Antiretroviral Therapy Initiation Determines Rectal Natural Killer Cell Populations

“…20 CD56 -CD16 + cells are terminally differentiated cells 21 that have fewer activating and more inhibitory receptors. 22 Thus, CD56 -CD16 + cells are ineffective, or at least less effective, at cytotoxicity and producing cytokines and chemokines including CCR5 ligands (CCL3, CCL4, and CCL5), 9,27 and some propose that their expansion, replacing more functional cells, may facilitate HIV-1 infection of CD4 + T cells. 9 Of note, CD56 -CD16 + NK cells can suppress IFN-c production by CD8 + T cells.…”

A NKp80-based identification strategy reveals that CD56negNK cells are not completely dysfunctional in health and disease

“…Furthermore, in healthy donors, both cytokine production and the degranulation capability were increased in the CD56 neg NKp80 + cells (Fig 3B). Our results indicate that, although CD56 neg NK cells have lower effector functions than CD56 dim NK cells (Fig EV6), their functionality might not be completely impaired [26].…”